import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
-import java.util.EnumSet;
import java.util.HashMap;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import jalview.analysis.AlignmentUtils;
+import jalview.api.structures.JalviewStructureDisplayI;
+import jalview.bin.Jalview.ExitCode;
import jalview.bin.argparser.Arg;
import jalview.bin.argparser.ArgParser;
import jalview.bin.argparser.ArgParser.Position;
import jalview.bin.argparser.ArgValue;
-import jalview.bin.argparser.ArgValues;
import jalview.bin.argparser.ArgValuesMap;
import jalview.bin.argparser.SubVals;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.annotations.AlphaFoldAnnotationRowBuilder;
import jalview.gui.AlignFrame;
import jalview.gui.AlignmentPanel;
+import jalview.gui.AppJmol;
import jalview.gui.Desktop;
import jalview.gui.Preferences;
import jalview.gui.StructureChooser;
import jalview.gui.StructureViewer;
import jalview.gui.StructureViewer.ViewerType;
import jalview.io.AppletFormatAdapter;
+import jalview.io.BackupFiles;
import jalview.io.BioJsHTMLOutput;
import jalview.io.DataSourceType;
import jalview.io.FileFormat;
import jalview.io.FileFormatException;
import jalview.io.FileFormatI;
+import jalview.io.FileFormats;
import jalview.io.FileLoader;
import jalview.io.HtmlSvgOutput;
import jalview.io.IdentifyFile;
+import jalview.io.NewickFile;
+import jalview.io.exceptions.ImageOutputException;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemeProperty;
import jalview.structure.StructureImportSettings.TFType;
import jalview.structure.StructureSelectionManager;
+import jalview.util.FileUtils;
import jalview.util.HttpUtils;
+import jalview.util.ImageMaker;
+import jalview.util.ImageMaker.TYPE;
import jalview.util.MessageManager;
import jalview.util.Platform;
+import jalview.util.imagemaker.BitmapImageSizing;
public class Commands
{
private Map<String, AlignFrame> afMap;
+ private Map<String, List<StructureViewer>> svMap;
+
private boolean commandArgsProvided = false;
private boolean argsWereParsed = false;
+ private List<String> errors = new ArrayList<>();
+
public Commands(ArgParser argparser, boolean headless)
{
this(Desktop.instance, argparser, headless);
argParser = argparser;
headless = h;
desktop = d;
- afMap = new HashMap<String, AlignFrame>();
- if (argparser != null)
- {
- processArgs(argparser, headless);
- }
+ afMap = new HashMap<>();
}
- private boolean processArgs(ArgParser argparser, boolean h)
+ protected boolean processArgs()
{
- argParser = argparser;
- headless = h;
+ if (argParser == null)
+ {
+ return true;
+ }
+
boolean theseArgsWereParsed = false;
if (argParser != null && argParser.getLinkedIds() != null)
{
ArgValuesMap avm = argParser.getLinkedArgs(id);
theseArgsWereParsed = true;
- theseArgsWereParsed &= processLinked(id);
+ boolean processLinkedOkay = processLinked(id);
+ theseArgsWereParsed &= processLinkedOkay;
+
+ processGroovyScript(id);
+
+ // wait around until alignFrame isn't busy
+ AlignFrame af = afMap.get(id);
+ while (af != null && af.getViewport().isCalcInProgress())
+ {
+ try
+ {
+ Thread.sleep(25);
+ } catch (Exception q)
+ {
+ }
+ ;
+ }
+
theseArgsWereParsed &= processImages(id);
+ if (processLinkedOkay)
+ {
+ theseArgsWereParsed &= processOutput(id);
+ }
+
// close ap
if (avm.getBoolean(Arg.CLOSE))
{
- AlignFrame af = afMap.get(id);
+ af = afMap.get(id);
if (af != null)
{
af.closeMenuItem_actionPerformed(true);
}
}
- if (argParser.getBool(Arg.QUIT))
+
+ // report errors
+ Console.warn(
+ "The following errors and warnings occurred whilst processing files:\n"
+ + errorsToString());
+ // gui errors reported in Jalview
+
+ if (argParser.getBoolean(Arg.QUIT))
{
- Jalview.getInstance().quit();
+ Jalview.getInstance().exit(
+ "Exiting due to " + Arg.QUIT.argString() + " argument.",
+ ExitCode.OK);
return true;
}
// carry on with jalview.bin.Jalview
return argsWereParsed;
}
- protected boolean processUnlinked(String id)
- {
- return processLinked(id);
- }
-
protected boolean processLinked(String id)
{
boolean theseArgsWereParsed = false;
ArgValuesMap avm = argParser.getLinkedArgs(id);
if (avm == null)
+ {
return true;
+ }
+
+ Boolean isError = Boolean.valueOf(false);
+
+ // set wrap scope here so it can be applied after structures are opened
+ boolean wrap = false;
- /*
- * // script to execute after all loading is completed one way or another String
- * groovyscript = m.get(Arg.GROOVY) == null ? null :
- * m.get(Arg.GROOVY).getValue(); String file = m.get(Arg.OPEN) == null ? null :
- * m.get(Arg.OPEN).getValue(); String data = null; FileFormatI format = null;
- * DataSourceType protocol = null;
- */
if (avm.containsArg(Arg.APPEND) || avm.containsArg(Arg.OPEN))
{
commandArgsProvided = true;
{
if (!(new File(openFile)).exists())
{
- Console.warn("Can't find file '" + openFile + "'");
+ addError("Can't find file '" + openFile + "'");
+ isError = true;
+ continue;
}
}
}
format = new IdentifyFile().identify(openFile, protocol);
} catch (FileFormatException e1)
{
- Console.error("Unknown file format for '" + openFile + "'");
+ addError("Unknown file format for '" + openFile + "'");
+ isError = true;
+ continue;
}
af = afMap.get(id);
if (af == null || "true".equals(av.getSubVal("new"))
|| a == Arg.OPEN || format == FileFormat.Jalview)
{
- /*
- * this approach isn't working yet // get default annotations before opening
- * AlignFrame if (m.get(Arg.SSANNOTATIONS) != null) {
- * Console.debug("##### SSANNOTATIONS=" + m.get(Arg.SSANNOTATIONS).getBoolean());
- * } if (m.get(Arg.NOTEMPFAC) != null) { Console.debug( "##### NOTEMPFAC=" +
- * m.get(Arg.NOTEMPFAC).getBoolean()); } boolean showSecondaryStructure =
- * (m.get(Arg.SSANNOTATIONS) != null) ? m.get(Arg.SSANNOTATIONS).getBoolean() :
- * false; boolean showTemperatureFactor = (m.get(Arg.NOTEMPFAC) != null) ?
- * !m.get(Arg.NOTEMPFAC).getBoolean() : false; Console.debug("##### tempfac=" +
- * showTemperatureFactor + ", showSS=" + showSecondaryStructure);
- * StructureSelectionManager ssm = StructureSelectionManager
- * .getStructureSelectionManager(Desktop.instance); if (ssm != null) {
- * ssm.setAddTempFacAnnot(showTemperatureFactor);
- * ssm.setProcessSecondaryStructure(showSecondaryStructure); }
- */
+ if (a == Arg.OPEN)
+ {
+ Jalview.testoutput(argParser, Arg.OPEN, "examples/uniref50.fa",
+ openFile);
+ }
Console.debug(
"Opening '" + openFile + "' in new alignment frame");
FileLoader fileLoader = new FileLoader(!headless);
+ boolean xception = false;
+ try
+ {
+ af = fileLoader.LoadFileWaitTillLoaded(openFile, protocol,
+ format);
+ } catch (Throwable thr)
+ {
+ xception = true;
+ addError("Couldn't open '" + openFile + "' as " + format + " "
+ + thr.getLocalizedMessage()
+ + " (Enable debug for full stack trace)");
+ isError = true;
+ Console.debug("Exception when opening '" + openFile + "'", thr);
+ } finally
+ {
+ if (af == null && !xception)
+ {
+ addInfo("Ignoring '" + openFile
+ + "' - no alignment data found.");
+ continue;
+ }
+ }
- af = fileLoader.LoadFileWaitTillLoaded(openFile, protocol,
- format);
- boolean showAnnotations = ArgParser.getFromSubValArgOrPref(avm,
- Arg.ANNOTATIONS, av.getSubVals(), null,
- "SHOW_ANNOTATIONS", true);
- af.setAnnotationsVisibility(showAnnotations, false, true);
-
- // wrap alignment?
- boolean wrap = ArgParser.getFromSubValArgOrPref(avm, Arg.WRAP, sv,
- null, "WRAP_ALIGNMENT", false);
- af.getCurrentView().setWrapAlignment(wrap);
-
- // colour aligment?
+ // colour alignment?
String colour = ArgParser.getFromSubValArgOrPref(avm, av,
Arg.COLOUR, sv, null, "DEFAULT_COLOUR_PROT", "");
-
if ("" != colour)
{
- af.changeColour_actionPerformed(colour);
+ ColourSchemeI cs = ColourSchemeProperty.getColourScheme(
+ af.getViewport(), af.getViewport().getAlignment(),
+ colour);
+
+ if (cs == null && !"None".equals(colour))
+ {
+ addWarn("Couldn't parse '" + colour + "' as a colourscheme.");
+ }
+ else
+ {
+ af.changeColour(cs);
+ }
+ Jalview.testoutput(argParser, Arg.COLOUR, "zappo", colour);
}
- // change alignment frame title
+ // Change alignment frame title
String title = ArgParser.getFromSubValArgOrPref(avm, av,
Arg.TITLE, sv, null, null, null);
if (title != null)
+ {
af.setTitle(title);
+ Jalview.testoutput(argParser, Arg.TITLE, "test title", title);
+ }
- // show secondary structure annotations?
- boolean showSSAnnotations = ArgParser.getFromSubValArgOrPref(avm,
- Arg.SSANNOTATIONS, av.getSubVals(), null,
- "STRUCT_FROM_PDB", true);
- if (avm.getBoolean(Arg.SSANNOTATIONS))
+ // Add features
+ String featuresfile = ArgParser.getValueFromSubValOrArg(avm, av,
+ Arg.FEATURES, sv);
+ if (featuresfile != null)
{
- af.setAnnotationsVisibility(showSSAnnotations, true, false);
- /*
- AlignmentUtils.showOrHideSequenceAnnotations(
- af.getCurrentView().getAlignment(),
- Collections.singleton("Secondary Structure"), null,
- false, false);
- */
+ af.parseFeaturesFile(featuresfile,
+ AppletFormatAdapter.checkProtocol(featuresfile));
+ Jalview.testoutput(argParser, Arg.FEATURES,
+ "examples/testdata/plantfdx.features", featuresfile);
+ }
+
+ // Add annotations from file
+ String annotationsfile = ArgParser.getValueFromSubValOrArg(avm,
+ av, Arg.ANNOTATIONS, sv);
+ if (annotationsfile != null)
+ {
+ af.loadJalviewDataFile(annotationsfile, null, null, null);
+ Jalview.testoutput(argParser, Arg.ANNOTATIONS,
+ "examples/testdata/plantfdx.annotations",
+ annotationsfile);
+ }
+
+ // Set or clear the sortbytree flag
+ boolean sortbytree = ArgParser.getBoolFromSubValOrArg(avm,
+ Arg.SORTBYTREE, sv);
+ if (sortbytree)
+ {
+ af.getViewport().setSortByTree(true);
+ Jalview.testoutput(argParser, Arg.SORTBYTREE);
}
+ // Load tree from file
+ String treefile = ArgParser.getValueFromSubValOrArg(avm, av,
+ Arg.TREE, sv);
+ if (treefile != null)
+ {
+ try
+ {
+ NewickFile nf = new NewickFile(treefile,
+ AppletFormatAdapter.checkProtocol(treefile));
+ af.getViewport().setCurrentTree(
+ af.showNewickTree(nf, treefile).getTree());
+ Jalview.testoutput(argParser, Arg.TREE,
+ "examples/testdata/uniref50_test_tree", treefile);
+ } catch (IOException e)
+ {
+ addError("Couldn't add tree " + treefile, e);
+ isError = true;
+ }
+ }
+
+ // Show secondary structure annotations?
+ boolean showSSAnnotations = ArgParser.getFromSubValArgOrPref(avm,
+ Arg.SHOWSSANNOTATIONS, av.getSubVals(), null,
+ "STRUCT_FROM_PDB", true);
+ af.setAnnotationsVisibility(showSSAnnotations, true, false);
+
+ // Show sequence annotations?
+ boolean showAnnotations = ArgParser.getFromSubValArgOrPref(avm,
+ Arg.SHOWANNOTATIONS, av.getSubVals(), null,
+ "SHOW_ANNOTATIONS", true);
+ af.setAnnotationsVisibility(showAnnotations, false, true);
+
// show temperature factor annotations?
if (avm.getBoolean(Arg.NOTEMPFAC))
{
af.getCurrentView().getAlignment(), hideThese, null,
false, false);
}
- else
- /*
- * comment out hacky approach up to here and add this line: if
- * (showTemperatureFactor)
- */
- {
- /*
- if (avm.containsArg(Arg.TEMPFAC_LABEL))
- {
- AlignmentAnnotation aa = AlignmentUtils
- .getFirstSequenceAnnotationOfType(
- af.getCurrentView().getAlignment(),
- AlignmentAnnotation.LINE_GRAPH);
- String label = avm.getValue(Arg.TEMPFAC_LABEL);
- if (aa != null)
- {
- aa.label = label;
- }
- else
- {
- Console.info(
- "Could not find annotation to apply tempfac_label '"
- + label);
- }
- }
- */
- }
+
+ // wrap alignment? do this last for formatting reasons
+ wrap = ArgParser.getFromSubValArgOrPref(avm, Arg.WRAP, sv, null,
+ "WRAP_ALIGNMENT", false);
+ // af.setWrapFormat(wrap) is applied after structures are opened for
+ // annotation reasons
// store the AlignFrame for this id
afMap.put(id, af);
{
if (headless)
{
- Jalview.exit("Could not open any files in headless mode", 1);
+ Jalview.exit("Could not open any files in headless mode",
+ ExitCode.NO_FILES);
}
else
{
- Console.warn("No more files to open");
+ Console.info("No more files to open");
}
}
if (progressBarSet && desktop != null)
{
String val = av.getValue();
SubVals subVals = av.getSubVals();
- SequenceI seq = getSpecifiedSequence(af, subVals);
+ SequenceI seq = getSpecifiedSequence(af, avm, av);
if (seq == null)
{
// Could not find sequence from subId, let's assume the first
if (seq == null)
{
- Console.warn("Could not find sequence for argument "
+ addWarn("Could not find sequence for argument "
+ Arg.STRUCTURE.argString() + "=" + val);
- // you probably want to continue here, not break
- // break;
continue;
}
File structureFile = null;
if (structureFile == null)
{
- Console.warn("Not provided structure file with '" + val + "'");
+ addWarn("Not provided structure file with '" + val + "'");
continue;
}
if (!structureFile.exists())
{
- Console.warn("Structure file '"
- + structureFile.getAbsoluteFile() + "' not found.");
+ addWarn("Structure file '" + structureFile.getAbsoluteFile()
+ + "' not found.");
continue;
}
Console.debug("Using structure file "
+ structureFile.getAbsolutePath());
- // ##### Does this need to happen? Follow
- // openStructureFileForSequence() below
- /*
- PDBEntry fileEntry = new AssociatePdbFileWithSeq()
- .associatePdbWithSeq(structureFile.getAbsolutePath(),
- DataSourceType.FILE, seq, true, Desktop.instance);
- */
-
// open structure view
AlignmentPanel ap = af.alignPanel;
if (headless)
String structureFilepath = structureFile.getAbsolutePath();
// get PAEMATRIX file and label from subvals or Arg.PAEMATRIX
- String paeFilepath = subVals.getWithSubstitutions(argParser, id,
- "paematrix");
- String paeLabel = subVals.get("paelabel");
- ArgValue paeAv = getArgAssociatedWithStructure(Arg.PAEMATRIX, avm,
- af, structureFilepath);
- if (paeFilepath == null && paeAv != null)
+ String paeFilepath = ArgParser
+ .getFromSubValArgOrPrefWithSubstitutions(argParser, avm,
+ Arg.PAEMATRIX, Position.AFTER, av, subVals, null,
+ null, null);
+ if (paeFilepath != null)
{
- SubVals sv = paeAv.getSubVals();
- File paeFile = new File(sv.getContent());
+ File paeFile = new File(paeFilepath);
- paeLabel = sv.get("label");
try
{
paeFilepath = paeFile.getCanonicalPath();
} catch (IOException e)
{
paeFilepath = paeFile.getAbsolutePath();
- Console.warn("Problem with the PAE file path: '"
+ addWarn("Problem with the PAE file path: '"
+ paeFile.getPath() + "'");
}
}
// showing annotations from structure file or not
boolean ssFromStructure = ArgParser.getFromSubValArgOrPref(avm,
- Arg.SSANNOTATIONS, subVals, null, "STRUCT_FROM_PDB",
+ Arg.SHOWSSANNOTATIONS, subVals, null, "STRUCT_FROM_PDB",
true);
// get TEMPFAC type from subvals or Arg.TEMPFAC in case user Adds
// reference annotations
- String tftString = subVals.get("tempfac");
- TFType tft = avm.getBoolean(Arg.NOTEMPFAC) ? null
- : TFType.DEFAULT;
- ArgValue tftAv = getArgAssociatedWithStructure(Arg.TEMPFAC, avm,
- af, structureFilepath);
- if (tftString == null && tftAv != null)
- {
- tftString = tftAv.getSubVals().getContent();
- }
- if (tftString != null)
+ String tftString = ArgParser
+ .getFromSubValArgOrPrefWithSubstitutions(argParser, avm,
+ Arg.TEMPFAC, Position.AFTER, av, subVals, null,
+ null, null);
+ boolean notempfac = ArgParser.getFromSubValArgOrPref(avm,
+ Arg.NOTEMPFAC, subVals, null, "ADD_TEMPFACT_ANN", false,
+ true);
+ TFType tft = notempfac ? null : TFType.DEFAULT;
+ if (tftString != null && !notempfac)
{
// get kind of temperature factor annotation
try
if (it.hasNext())
sb.append(", ");
}
- Console.warn(sb.toString());
+ addWarn(sb.toString());
}
}
String sViewer = ArgParser.getFromSubValArgOrPref(avm,
- Arg.STRUCTUREVIEWER, Position.AFTER, av, subVals,
- "viewer", null, "jmol");
- ViewerType viewerType = null;
- if (!"none".equals(sViewer))
+ Arg.STRUCTUREVIEWER, Position.AFTER, av, subVals, null,
+ null, "jmol");
+ ViewerType viewerType = ViewerType.getFromString(sViewer);
+
+ // TODO use ssFromStructure
+ StructureViewer sv = StructureChooser
+ .openStructureFileForSequence(null, null, ap, seq, false,
+ structureFilepath, tft, paeFilepath, false,
+ ssFromStructure, false, viewerType);
+
+ if (sv == null)
{
- for (ViewerType v : EnumSet.allOf(ViewerType.class))
+ addError("Failed to import and open structure view for file '"
+ + structureFile + "'.");
+ continue;
+ }
+ try
+ {
+ long tries = 1000;
+ while (sv.isBusy() && tries > 0)
{
- String name = v.name().toLowerCase(Locale.ROOT)
- .replaceAll(" ", "");
- if (sViewer.equals(name))
+ Thread.sleep(25);
+ if (sv.isBusy())
{
- viewerType = v;
- break;
+ tries--;
+ Console.debug(
+ "Waiting for viewer for " + structureFilepath);
}
}
+ if (tries == 0 && sv.isBusy())
+ {
+ addWarn("Gave up waiting for structure viewer to load file '"
+ + structureFile
+ + "'. Something may have gone wrong.");
+ }
+ } catch (Exception x)
+ {
+ addError("Exception whilst waiting for structure viewer "
+ + structureFilepath, x);
+ isError = true;
}
- boolean addTempFac = tft != null
- || Cache.getDefault("ADD_TEMPFACT_ANN", false);
+ // add StructureViewer to svMap list
+ if (svMap == null)
+ {
+ svMap = new HashMap<>();
+ }
+ if (svMap.get(id) == null)
+ {
+ svMap.put(id, new ArrayList<>());
+ }
+ svMap.get(id).add(sv);
- // TODO use ssFromStructure
- StructureChooser.openStructureFileForSequence(null, null, ap, seq,
- false, structureFilepath, tft, paeFilepath, false,
- ssFromStructure, false, viewerType);
+ Console.debug(
+ "Successfully opened viewer for " + structureFilepath);
+ String structureImageFilename = ArgParser.getValueFromSubValOrArg(
+ avm, av, Arg.STRUCTUREIMAGE, subVals);
+ if (sv != null && structureImageFilename != null)
+ {
+ ArgValue siAv = avm.getClosestNextArgValueOfArg(av,
+ Arg.STRUCTUREIMAGE);
+ SubVals sisv = null;
+ if (structureImageFilename.equals(siAv.getValue()))
+ {
+ sisv = siAv.getSubVals();
+ }
+ File structureImageFile = new File(structureImageFilename);
+ String width = ArgParser.getValueFromSubValOrArg(avm, av,
+ Arg.STRUCTUREIMAGEWIDTH, sisv);
+ String height = ArgParser.getValueFromSubValOrArg(avm, av,
+ Arg.STRUCTUREIMAGEHEIGHT, sisv);
+ String scale = ArgParser.getValueFromSubValOrArg(avm, av,
+ Arg.STRUCTUREIMAGESCALE, sisv);
+ String renderer = ArgParser.getValueFromSubValOrArg(avm, av,
+ Arg.STRUCTUREIMAGETEXTRENDERER, sisv);
+ String typeS = ArgParser.getValueFromSubValOrArg(avm, av,
+ Arg.STRUCTUREIMAGETYPE, sisv);
+ if (typeS == null || typeS.length() == 0)
+ {
+ typeS = FileUtils.getExtension(structureImageFile);
+ }
+ TYPE imageType;
+ try
+ {
+ imageType = Enum.valueOf(TYPE.class,
+ typeS.toUpperCase(Locale.ROOT));
+ } catch (IllegalArgumentException e)
+ {
+ addWarn("Do not know image format '" + typeS
+ + "', using PNG");
+ imageType = TYPE.PNG;
+ }
+ BitmapImageSizing userBis = ImageMaker
+ .parseScaleWidthHeightStrings(scale, width, height);
+ // TODO MAKE THIS VIEWER INDEPENDENT!!
+ switch (StructureViewer.getViewerType())
+ {
+ case JMOL:
+ JalviewStructureDisplayI sview = sv
+ .getJalviewStructureDisplay();
+ if (sview instanceof AppJmol)
+ {
+ AppJmol jmol = (AppJmol) sview;
+ try
+ {
+ boolean success = this.checksBeforeWritingToFile(avm,
+ subVals, false, structureImageFilename,
+ "structure image", isError);
+ if (!success)
+ {
+ continue;
+ }
+
+ Console.debug("Rendering image to " + structureImageFile);
+ jmol.makePDBImage(structureImageFile, imageType, renderer,
+ userBis);
+ Console.debug("Finished Rendering image to "
+ + structureImageFile);
+
+ } catch (ImageOutputException ioexc)
+ {
+ addError("Unexpected error whilst exporting image to "
+ + structureImageFile, ioexc);
+ isError = true;
+ continue;
+ }
+
+ }
+ break;
+ default:
+ addWarn("Cannot export image for structure viewer "
+ + sv.getViewerType() + " yet");
+ continue;
+ }
+ }
}
}
}
+ if (wrap)
+ {
+ AlignFrame af = afMap.get(id);
+ if (af != null)
+ {
+ af.setWrapFormat(wrap, true);
+ }
+ }
+
/*
boolean doShading = avm.getBoolean(Arg.TEMPFAC_SHADING);
if (doShading)
}
*/
- return theseArgsWereParsed;
+ return theseArgsWereParsed && !isError;
+ }
+
+ protected void processGroovyScript(String id)
+ {
+ ArgValuesMap avm = argParser.getLinkedArgs(id);
+ AlignFrame af = afMap.get(id);
+
+ if (af == null)
+ {
+ addWarn("Did not have an alignment window for id=" + id);
+ return;
+ }
+
+ if (avm.containsArg(Arg.GROOVY))
+ {
+ String groovyscript = avm.getValue(Arg.GROOVY);
+ if (groovyscript != null)
+ {
+ // Execute the groovy script after we've done all the rendering stuff
+ // and before any images or figures are generated.
+ Console.info("Executing script " + groovyscript);
+ Jalview.getInstance().executeGroovyScript(groovyscript, af);
+ }
+ }
}
protected boolean processImages(String id)
if (af == null)
{
- Console.warn("Did not have an alignment window for id=" + id);
+ addWarn("Did not have an alignment window for id=" + id);
return false;
}
+ Boolean isError = Boolean.valueOf(false);
if (avm.containsArg(Arg.IMAGE))
{
for (ArgValue av : avm.getArgValueList(Arg.IMAGE))
{
String val = av.getValue();
SubVals subVal = av.getSubVals();
- String type = "png"; // default
String fileName = subVal.getContent();
File file = new File(fileName);
+ String name = af.getName();
String renderer = ArgParser.getValueFromSubValOrArg(avm, av,
- Arg.RENDERER, subVal);
+ Arg.TEXTRENDERER, subVal);
if (renderer == null)
renderer = "text";
+ String type = "png"; // default
+
+ String scale = ArgParser.getValueFromSubValOrArg(avm, av, Arg.SCALE,
+ subVal);
+ String width = ArgParser.getValueFromSubValOrArg(avm, av, Arg.WIDTH,
+ subVal);
+ String height = ArgParser.getValueFromSubValOrArg(avm, av,
+ Arg.HEIGHT, subVal);
+ BitmapImageSizing userBis = ImageMaker
+ .parseScaleWidthHeightStrings(scale, width, height);
+
type = ArgParser.getValueFromSubValOrArg(avm, av, Arg.TYPE, subVal);
if (type == null && fileName != null)
{
Cache.setPropsAreReadOnly(true);
Cache.setProperty("EXPORT_EMBBED_BIOJSON", "false");
- switch (type)
- {
+ Console.info("Writing " + file);
- case "svg":
- Console.debug("Outputting type '" + type + "' to " + fileName);
- af.createSVG(file, renderer);
- break;
-
- case "png":
- Console.debug("Outputting type '" + type + "' to " + fileName);
- af.createPNG(file);
- break;
-
- case "html":
- Console.debug("Outputting type '" + type + "' to " + fileName);
- HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
- htmlSVG.exportHTML(fileName, renderer);
- break;
+ boolean success = checksBeforeWritingToFile(avm, subVal, false,
+ fileName, "image", isError);
+ if (!success)
+ {
+ continue;
+ }
- case "biojs":
- try
- {
- BioJsHTMLOutput.refreshVersionInfo(
- BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
- } catch (URISyntaxException e)
+ try
+ {
+ switch (type)
{
- e.printStackTrace();
- }
- BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
- bjs.exportHTML(fileName);
- Console.debug("Creating BioJS MSA Viwer HTML file: " + fileName);
- break;
- default:
- Console.warn(Arg.IMAGE.argString() + " type '" + type
- + "' not known. Ignoring");
- break;
+ case "svg":
+ Console.debug("Outputting type '" + type + "' to " + fileName);
+ af.createSVG(file, renderer);
+ break;
+
+ case "png":
+ Console.debug("Outputting type '" + type + "' to " + fileName);
+ af.createPNG(file, null, userBis);
+ break;
+
+ case "html":
+ Console.debug("Outputting type '" + type + "' to " + fileName);
+ HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
+ htmlSVG.exportHTML(fileName, renderer);
+ break;
+
+ case "biojs":
+ Console.debug(
+ "Outputting BioJS MSA Viwer HTML file: " + fileName);
+ try
+ {
+ BioJsHTMLOutput.refreshVersionInfo(
+ BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
+ } catch (URISyntaxException e)
+ {
+ e.printStackTrace();
+ }
+ BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
+ bjs.exportHTML(fileName);
+ break;
+
+ case "eps":
+ Console.debug("Outputting EPS file: " + fileName);
+ af.createEPS(file, renderer);
+ break;
+
+ case "imagemap":
+ Console.debug("Outputting ImageMap file: " + fileName);
+ af.createImageMap(file, name);
+ break;
+
+ default:
+ addWarn(Arg.IMAGE.argString() + " type '" + type
+ + "' not known. Ignoring");
+ break;
+ }
+ } catch (Exception ioex)
+ {
+ addError("Unexpected error during export to '" + fileName + "'",
+ ioex);
+ isError = true;
}
}
}
- return true;
+ return !isError;
}
- private SequenceI getSpecifiedSequence(AlignFrame af, SubVals subId)
+ protected boolean processOutput(String id)
{
- if (subId == null)
- return null;
- AlignmentI al = af.getCurrentView().getAlignment();
- if (subId.has("seqid"))
- {
- return al.findName(subId.get("seqid"));
- }
- else if (-1 < subId.getIndex()
- && subId.getIndex() < al.getSequences().size())
+ ArgValuesMap avm = argParser.getLinkedArgs(id);
+ AlignFrame af = afMap.get(id);
+
+ if (af == null)
{
- return al.getSequenceAt(subId.getIndex());
+ addWarn("Did not have an alignment window for id=" + id);
+ return false;
}
- return null;
- }
- // returns the first Arg value intended for the structure structFilename
- // (in the given AlignFrame from the ArgValuesMap)
- private ArgValue getArgAssociatedWithStructure(Arg arg, ArgValuesMap avm,
- AlignFrame af, String structFilename)
- {
- if (af != null)
+ Boolean isError = Boolean.valueOf(false);
+
+ if (avm.containsArg(Arg.OUTPUT))
{
- for (ArgValue av : avm.getArgValueList(arg))
+ for (ArgValue av : avm.getArgValueList(Arg.OUTPUT))
{
+ String val = av.getValue();
SubVals subVals = av.getSubVals();
- String structid = subVals.get("structid");
- String structfile = subVals.get("structfile");
+ String fileName = subVals.getContent();
+ boolean stdout = ArgParser.STDOUTFILENAME.equals(fileName);
+ File file = new File(fileName);
- // let's find a structure
- if (structfile == null && structid == null)
+ String name = af.getName();
+ String format = ArgParser.getValueFromSubValOrArg(avm, av,
+ Arg.FORMAT, subVals);
+ FileFormats ffs = FileFormats.getInstance();
+ List<String> validFormats = ffs.getWritableFormats(false);
+
+ FileFormatI ff = null;
+ if (format == null && fileName != null)
{
- ArgValue likelyStructure = avm.getClosestPreviousArgValueOfArg(av,
- Arg.STRUCTURE);
- if (likelyStructure != null)
+ FORMAT: for (String fname : validFormats)
{
- SubVals sv = likelyStructure.getSubVals();
- if (sv != null && sv.has(ArgValues.ID))
+ FileFormatI tff = ffs.forName(fname);
+ String[] extensions = tff.getExtensions().split(",");
+ for (String ext : extensions)
{
- structid = sv.get(ArgValues.ID);
+ if (fileName.toLowerCase(Locale.ROOT).endsWith("." + ext))
+ {
+ ff = tff;
+ format = ff.getName();
+ break FORMAT;
+ }
}
- else
+ }
+ }
+ if (ff == null && format != null)
+ {
+ ff = ffs.forName(format);
+ }
+ if (ff == null)
+ {
+ if (stdout)
+ {
+ ff = FileFormat.Fasta;
+ }
+ else
+ {
+ StringBuilder validSB = new StringBuilder();
+ for (String f : validFormats)
{
- structfile = likelyStructure.getValue();
+ if (validSB.length() > 0)
+ validSB.append(", ");
+ validSB.append(f);
+ FileFormatI tff = ffs.forName(f);
+ validSB.append(" (");
+ validSB.append(tff.getExtensions());
+ validSB.append(")");
}
+
+ addError("No valid format specified for "
+ + Arg.OUTPUT.argString() + ". Valid formats are "
+ + validSB.toString() + ".");
+ continue;
}
}
- if (structfile == null && structid != null)
+ boolean success = checksBeforeWritingToFile(avm, subVals, true,
+ fileName, ff.getName(), isError);
+ if (!success)
{
- StructureSelectionManager ssm = StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance);
- if (ssm != null)
- {
- structfile = ssm.findFileForPDBId(structid);
- }
+ continue;
+ }
+
+ boolean backups = ArgParser.getFromSubValArgOrPref(avm, Arg.BACKUPS,
+ subVals, null,
+ Platform.isHeadless() ? null : BackupFiles.ENABLED,
+ !Platform.isHeadless());
+
+ Console.info("Writing " + fileName);
+
+ af.saveAlignment(fileName, ff, stdout, backups);
+ if (af.isSaveAlignmentSuccessful())
+ {
+ Console.debug("Written alignment '" + name + "' in "
+ + ff.getName() + " format to '" + file + "'");
+ }
+ else
+ {
+ addError("Error writing file '" + file + "' in " + ff.getName()
+ + " format!");
+ isError = true;
+ continue;
}
- if (structfile != null && structfile.equals(structFilename))
+
+ }
+ }
+ return !isError;
+ }
+
+ private SequenceI getSpecifiedSequence(AlignFrame af, ArgValuesMap avm,
+ ArgValue av)
+ {
+ SubVals subVals = av.getSubVals();
+ ArgValue idAv = avm.getClosestNextArgValueOfArg(av, Arg.SEQID);
+ SequenceI seq = null;
+ if (subVals == null && idAv == null)
+ return null;
+ if (af == null || af.getCurrentView() == null)
+ {
+ return null;
+ }
+ AlignmentI al = af.getCurrentView().getAlignment();
+ if (al == null)
+ {
+ return null;
+ }
+ if (subVals != null)
+ {
+ if (subVals.has(Arg.SEQID.getName()))
+ {
+ seq = al.findName(subVals.get(Arg.SEQID.getName()));
+ }
+ else if (-1 < subVals.getIndex()
+ && subVals.getIndex() < al.getSequences().size())
+ {
+ seq = al.getSequenceAt(subVals.getIndex());
+ }
+ }
+ if (seq == null && idAv != null)
+ {
+ seq = al.findName(idAv.getValue());
+ }
+ return seq;
+ }
+
+ public AlignFrame[] getAlignFrames()
+ {
+ AlignFrame[] afs = null;
+ if (afMap != null)
+ {
+ afs = (AlignFrame[]) afMap.values().toArray();
+ }
+
+ return afs;
+ }
+
+ public List<StructureViewer> getStructureViewers()
+ {
+ List<StructureViewer> svs = null;
+ if (svMap != null)
+ {
+ for (List<StructureViewer> svList : svMap.values())
+ {
+ if (svs == null)
{
- return av;
+ svs = new ArrayList<>();
}
+ svs.addAll(svList);
}
}
- return null;
+ return svs;
+ }
+
+ private void addInfo(String errorMessage)
+ {
+ Console.info(errorMessage);
+ errors.add(errorMessage);
+ }
+
+ private void addWarn(String errorMessage)
+ {
+ Console.warn(errorMessage);
+ errors.add(errorMessage);
+ }
+
+ private void addError(String errorMessage)
+ {
+ addError(errorMessage, null);
+ }
+
+ private void addError(String errorMessage, Exception e)
+ {
+ Console.error(errorMessage, e);
+ errors.add(errorMessage);
+ }
+
+ private boolean checksBeforeWritingToFile(ArgValuesMap avm,
+ SubVals subVal, boolean includeBackups, String filename,
+ String adjective, Boolean isError)
+ {
+ File file = new File(filename);
+
+ boolean overwrite = ArgParser.getFromSubValArgOrPref(avm, Arg.OVERWRITE,
+ subVal, null, "OVERWRITE_OUTPUT", false);
+ boolean stdout = false;
+ boolean backups = false;
+ if (includeBackups)
+ {
+ stdout = ArgParser.STDOUTFILENAME.equals(filename);
+ // backups. Use the Arg.BACKUPS or subval "backups" setting first,
+ // otherwise if headless assume false, if not headless use the user
+ // preference with default true.
+ backups = ArgParser.getFromSubValArgOrPref(avm, Arg.BACKUPS, subVal,
+ null, Platform.isHeadless() ? null : BackupFiles.ENABLED,
+ !Platform.isHeadless());
+ }
+
+ if (file.exists() && !(overwrite || backups || stdout))
+ {
+ addWarn("Won't overwrite file '" + filename + "' without "
+ + Arg.OVERWRITE.argString()
+ + (includeBackups ? " or " + Arg.BACKUPS.argString() : "")
+ + " set");
+ return false;
+ }
+
+ boolean mkdirs = ArgParser.getFromSubValArgOrPref(avm, Arg.MKDIRS,
+ subVal, null, "MKDIRS_OUTPUT", false);
+
+ if (!FileUtils.checkParentDir(file, mkdirs))
+ {
+ addError("Directory '"
+ + FileUtils.getParentDir(file).getAbsolutePath()
+ + "' does not exist for " + adjective + " file '" + filename
+ + "'."
+ + (mkdirs ? "" : " Try using " + Arg.MKDIRS.argString()));
+ isError = true;
+ return false;
+ }
+
+ return true;
+ }
+
+ public List<String> getErrors()
+ {
+ return errors;
+ }
+
+ public String errorsToString()
+ {
+ StringBuilder sb = new StringBuilder();
+ for (String error : errors)
+ {
+ if (sb.length() > 0)
+ sb.append("\n");
+ sb.append("- " + error);
+ }
+ return sb.toString();
}
}
git://source.jalview.org / jalview.git / blobdiff